Issue 3, 2015

Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position

Abstract

We report herein the possibility of modulating the structure of hairpin oligonucleotides (ODNs) by light exposure. By using 4,4′-dihydroxyl azobenzene derivatives as suitable linker units, the hairpin conformation can be photocontrolled in a reversible manner. To determine which cross-links show the largest photoswitching effect, 4,4′-bis(hydroxymethyl)azobenzene (Az1) and 4,4′-bis(hydroxyethyl)azobenzene (Az2) were designed and used to replace the loops of ODN hairpins. When Az1 was introduced to the loop of ODN hairpins with 4, 5 and 6 base pairs, the thermodynamic stability of the ODN hairpins decreased and the differences in Tm values from trans to cis were 12.1–24.1 °C, although this did not happen for Az2-ODN hairpins. CD results indicated that the azobenzene-modified hairpins displayed strong induced CD signals in the range of 300–350 nm and 400–450 nm. Thermodynamic parameters showed that the enthalpic change (−ΔH°) and the entropic change (−TΔS°) for trans to cis isomerization of Az1-ODNs 5a, 6a and 8a significantly decreased with a decrease in Tm values, whereas −ΔH° and −TΔS° for Az2-ODNs 5b and 6b clearly increased in spite of little change in Tm values. Quantum chemical calculation further explained that the stabilities of the trans form are much higher than their cis form for Az1-ODNs, but not for Az2-ODNs.

Graphical abstract: Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position

Supplementary files

Article information

Article type
Concise Article
Submitted
04 Sep 2014
Accepted
12 Dec 2014
First published
15 Dec 2014

Med. Chem. Commun., 2015,6, 461-468

Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position

L. Wu, Y. Wu, H. Jin, L. Zhang, Y. He and X. Tang, Med. Chem. Commun., 2015, 6, 461 DOI: 10.1039/C4MD00378K

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